I hope this isn't too late for you to read this...
To summarise, our mission team held chapel services at two schools, make a new sign for the church, helped prepare crafts for VBS, helped with church services and youth group/sunday school, testimonies, evangelism in the local park, helped with several tasks at the Japan Bible Home (campsite), and sightseeing. I think you'll really enjoy it; it is lots of fun. Good times.
Don't worry too much about the language barrier - provided you have Japanese/English speaking person helping your mission team!
The three key phrases are:
arigatou gozaimasu - thankyou (more formal - say it when you pay for things at the checkout)
sumimasen - excuse me (excuse me, I'm about to be rude - future)
gomen nasai - sorry (sorry for just being rude - past)
I've done some Japanese, so I know more than the basic stuff, but I found it useful to keep a notebook of new phrases/words I had learned or ones I had forgotten. Here's some of the more useful ones from there (I didn't write in a whole lot of useful ones I already knew, so you should probably read these along with a list of useful phrases.):
dou itashimashite - you're welcome
hajimemashite - nice to meet you
irasshaimase - I'm available to help you if you need it (said by shop assistant as you walk into a shop)
onegai shimasu - please do this...
~te kurete arigatou gozaimasu - thankyou for ~
yaki - grilled
niku - meat
gaijin - foreigner (that's you)
mondai - problem (mondai ga arimasen - not a problem)
shitsureisuru desu ga ~ - sorry for being rude, but ~
tomare - stop
shiru - to know
omoidasu - to remember
wasureru - to forget (wasuretta - I've forgotten)
tsukuru (作る )- to make
tsukau (使う )- to use
oshieru (教える )- to teach
rikaisu - to understand
mizu - water
shashin o totte moiidesuka? - may I take a photo?
otearai - toilet
atteimasu ka? - is that correct? (as in "[your attempt at asking something/replying in Japanese, and not sure if you said it correctly]. atteimasu ka?" Then they will say "hai" or correct you.)
otoko (男 )- man
onna (女 ) - woman
jujika - cross
denwa o kakeru - call on phone
tsukaireta - tired
isokashii - busy
shizukanishite - be quite
kyokai - church
saisho - first
subete - all
subarashii - wonderful
suteki - nice
~ ka ~ - ~ or ~
sasagemasu - to give (to higher)
agemasu - to give (to peer)
Don't worry too much about the Japanese toilets; I was never in a situation where there wasn't a Western toilet around, and if all else fails, the disabled toilet is always Western.
Also, don't blow your nose in public. If you do, use a tissue and throw it away. And keep a spare handkerchief in your pocket for drying your hands after using public toilets because many don't have electric driers or paper towels.
It is hot and humid, and you find people giving away cardboard fans with advertising and band aids and tissues and stuff; do take these as you'll find them useful. And people don't really eat or drink "on the go" or at all much in public, so just discreetly drink from your water bottle!
Transport - the train system is very efficient. If you plan to do a lot of travelling, get a Suica card (pronounced Swee-ka) so you don't need to work out the ticket price (the price is determined only by the distance travelled from point A to B). They cost 2000 yen (probably about $17-18 USD) and come with 600 yen credit on it. Then you charge it up when it runs out. But it become a more cost effective the more you travel. If you are only planning to do a bit of train travelling, you might want to just buy tickets as you need them. And if unsure, buy the smallest ticket and you can pay the difference at the 'ticket adjustment' places as you exit the station.
Shopping - look out for Seiyu (owned by Walmart). That's where you'll probably do the majority of your shopping. Also look out for 100 yen shops. Also second hand shops are great and the majority the things there are unopened or not used much (the one near us was called Second Street). And Aquarius will become your new favourite drink.
Japan has many things that are closer to the US way (eg. churches are usually run by Americans, power points are like US ones, but are mostly two pin, .... there's more, but I can't think of it), so you'll have less adjusting than we did. But they do drive on "the wrong side" in Japan. And everything is in km/hr.
So.. yeah... this is long and you'll probably want to print it off and read it on the plane. Have fun and God bless!!
EDIT: Oh, and Christian churches are a rarity, so take a photo when you see them while walking (we did!).
Also, Google Earth is fun to play with to work out where you've been.